Johnathan Ekong attended a Bible school of the Qua Iboe Mission in the 1920s and served as an evangelist. After the Ibesikpo group left the Qua Iboe, they commissioned Ekong to find a mission church in the U.S. while he was there getting his higher education. At Immanuel Lutheran College in North Carolina Ekong connected with the President of the school, Rev. Henry Nau. And Nau urged the Synodical Conference of North America to choose Nigeria for its first mission to Africa. Dr. Nau went to the field to get things organized in 1936. By the next year, Dr. William Schweppe arrived in Nigeria to serve as the head of the mission. Churches, schools, a worker-training school, and hospital were opened. The resulting Evangelical Lutheran Church of Nigeria grew to tens of thousands. After ELS and WELS broke off their fellowship with LC-MS, the Lutheran Church of Nigeria chose to remain partners with LC-MS.

In 1969 a group of nine churches and three pastors in the Otoro District broke from the Lutheran Church in Nigeria over issues such as fellowship with the Lutheran World Federation. Appeals were directed to the WELS to restore their fellowship with what was now named Christ the King Lutheran Church of Nigeria. The leader of CKLCN attended the WELS seminary in 1974. Teaching visits were made in 1977, 1980, and 1981. WELS and CKLCN declared mutual fellowship in 1981. After that teaching visits were made to Nigeria twice per year when possible.

Missionaries L. Schlomer and H. Johne taught seminary classes, preparing seven new pastors for ordination in 1994. The seminary was restarted in 2001 involving Nigerian pastors and WELS visiting pastors as instructors. Students came from All Saints Lutheran Church of Nigeria in Cross River State for joint classes. Christ the King Lutheran Seminary graduated seven in 2004, ten in 2008, and nine in 2015. The majority of recent students comes from All Saints Lutheran Church.

The main cluster of CKLCN congregations lie in a triangle in Akwa Ibom State, with points at Uyo, Abak, and Ikot Ekpene. One congregation meets in Port Harcourt in Rivers State. Six congregations are in Calabar and rural areas around this major city in Cross River State.

CKLCN has a busy system leaders, organizations, boards and committees, including a Development Committee, a Mission Board, and a Welfare Committee. The congregations have benefited from a variety of humanitarian aid grants from WELS Christian Aid and Relief.

Two representatives of CKLCN attended the African Regional CELS conference in Lusaka in 2012. The synod president attended the regional meeting in Lilongwe in 2015. CKLCN is scheduled to host the African Regional CELC meeting in 2018. For 20 years to date efforts to secure visas for Nigerians to attend the larger international CELC conferences have been denied by host countries. Finances also limit efforts to attend.

No WELS missionary lives in Nigeria. D. Weiser, the current WELS missionary, will retire in June 2017. WELS is calling a replacement, who will be missionary to both Nigeria and Cameroon.